The purpose of this study focused on molecular mechanism under low temperature of homologous diploid and tetraploid watermelon seeding. Homologous diploid and tetraploid of female Jingxin 83166 were used as materials. Genes different expression using MSAP andlevel were analysised under low temperature stress and different bands were selected to be cloned, sequenced and compared.A total of 1564 locus were amplied using 22 MSAP primer combinations. Declining levels in the total methylation was 2.8% and 6.4% of the diploid and the tetraploid of watermelon, respectively. Blast 12 different bands in watermelon genome database,and 7 bands were identified as watermelon genome sequence. After being screened with 26 cDNA-AFLP primer combinations, 1267 bands were amplied, including 48.2% with up-regulated expression, 51.8% with down-regulated expression in the diploid of watermelon,58.6% with up-regulated expression,41.4% with down-regulated expression in the tetraploid of watermelon. NCBI Blast search showed that 23 bands were homologous functional genes,including hypothetical protein（39.13%）,energy and metabolism protein（43.48%）,material transportation protein（8.70%）,transcription relation protein（4.35%）and stress-related protein（4.35%），and other 10 bands with remained unknown function. Under low temperature stress,the methylation rate and up-regulated genes of the tetraploid of watermelon were greater than the diploid of watermelon, the tetraploid of watermelon induced genes involved in energy and metabolism and stress-related process, illustrating that the tetraploid of watermelon had stronger resistance than the diploid of watermelon.